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Recent Advances in Molecular Computational Chemistry
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Recent Advances in Molecular Computational Chemistry

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Computational and Theoretical Chemistry".

Deadline for manuscript submissions: closed (31 March 2024) | Viewed by 16754

Special Issue Editors

Prof. Dr. Weiwei Han

E-Mail Website
Guest Editor
Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun 130012, China
Interests: the relationship between enzyme structure and function; computer-aided drug design; computational structural biology; machine learning
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Lihong Hu

E-Mail Website
Guest Editor
School of Information Science and Technology, Northeast Normal University, Changchun 130117, China
Interests: computational chemistry; artificial intelligence; deep learning; chemical databases; quantum chemistry
Special Issues, Collections and Topics in MDPI journals
Dr. Juexin Wang

E-Mail Website
Guest Editor
School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46203, USA
Interests: machine learning; deep learning; bioinformatics; data analysis; graph representation learning; single cell sequencing

Special Issue Information

Dear Colleagues,

Theoretical approaches (molecular docking, molecular dynamics simulations, quantum mechanics/molecular mechanics, etc.) are a new crossover tool emerging with the development of chemistry and computer science and technology. They have a variety of applications, including in molecular design, classifying the components of complicated compound systems, and studying the molecular mechanics of chemical reactions. This Special Issue aims to review the latest research trends in molecular computational chemistry. By collecting contributions from scientists specializing in the field, this issue will provide an overview of the latest advances and newest knowledge in various fields where computer technology has been combined with chemistry. We invite authors to draw on computational chemistry to study a variety of fields.  

We look forward to receiving your submissions of original research articles and review articles.

Prof. Dr. Weiwei Han
Prof. Dr. Lihong Hu
Dr. Juexin Wang
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular design
  • computational chemistry
  • cheminformatics
  • data mining
  • molecular dynamics simulations

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Published Papers (7 papers)

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Research

16 pages, 4053 KiB  
Article
Unveiling the Anti-Cholera and Active Diabetic Renoprotective Compounds of Maqian Essential Oil: A Computational and Molecular Dynamics Study
by Mahmoud Dahab, Ping Zhang, Samiah Hamad Al-Mijalli and Emad M. Abdallah
Molecules 2023, 28(24), 7954; https://doi.org/10.3390/molecules28247954 - 5 Dec 2023
Cited by 1 | Viewed by 1991
Abstract
Cholera is an exceptionally aggressive infectious disease characterized by the potential to induce acute, copious, watery diarrhea of considerable severity and renal inflammation. Diabetic nephropathy is a serious complication of diabetes mellitus that can lead to kidney failure through inflammation; thus, anti-inflammatory agents [...] Read more.
Cholera is an exceptionally aggressive infectious disease characterized by the potential to induce acute, copious, watery diarrhea of considerable severity and renal inflammation. Diabetic nephropathy is a serious complication of diabetes mellitus that can lead to kidney failure through inflammation; thus, anti-inflammatory agents are promising therapies for diabetic nephropathy. Previous studies have shown that the essential oil of Zanthoxylum myriacanthum var. pubescens Huang, Maqian essential oil (MQEO), exhibits potent antibacterial, anti-inflammatory, and renoprotective activities in diabetic mice and has emerged as a potential therapeutic drug for the treatment of diabetic nephropathy complications. Therefore, the present study was carried out to screen the potential inhibition of cholera toxin and the diabetic renoprotective activity of MQEO through computational approaches. Twelve chemical constituents derived from MQEO were docked with cholera toxin and the target proteins involved in diabetic nephropathy, namely, TXNIP, Nrf2, and DPP IV, and, subsequently, the predictions of molecular dynamic simulations, the drug-likeness properties, and the ADMET properties were performed. α-terpineol showed high binding affinities toward the cholera toxin protein. For TXNIP, among all the chemical constituents, α-phellandrene and p-cymene showed strong binding affinities with the TXNIP protein and displayed relatively stable flexibility at the hinge regions of the protein, favorable physicochemical properties in the absence of hepatotoxicity, and low cytotoxicity. For Nrf2, α-terpineol exhibited the highest binding affinity and formed a very stable complex with Nrf2, which displayed high pharmacokinetic properties. All compounds had low free-binding energies when docked with the DPP IV protein, which suggests potent biological activity. In conclusion, based on a computational approach, our findings reveal that MQEO constituents have inhibitory activity against cholera toxin and are promising therapeutic agents for suppressing diabetic inflammation and for the treatment of diabetic nephropathy complications. Full article
(This article belongs to the Special Issue Recent Advances in Molecular Computational Chemistry)
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14 pages, 4018 KiB  
Article
The Effect of Ethanol on Lipid Nanoparticle Stabilization from a Molecular Dynamics Simulation Perspective
by Ari Hardianto, Zahra Silmi Muscifa, Wahyu Widayat, Muhammad Yusuf and Toto Subroto
Molecules 2023, 28(12), 4836; https://doi.org/10.3390/molecules28124836 - 17 Jun 2023
Cited by 5 | Viewed by 3987
Abstract
Lipid nanoparticles (LNPs) have emerged as a promising delivery system, particularly for genetic therapies and vaccines. LNP formation requires a specific mixture of nucleic acid in a buffered solution and lipid components in ethanol. Ethanol acts as a lipid solvent, aiding the formation [...] Read more.
Lipid nanoparticles (LNPs) have emerged as a promising delivery system, particularly for genetic therapies and vaccines. LNP formation requires a specific mixture of nucleic acid in a buffered solution and lipid components in ethanol. Ethanol acts as a lipid solvent, aiding the formation of the nanoparticle’s core, but its presence can also affect LNP stability. In this study, we used molecular dynamics (MD) simulations to investigate the physicochemical effect of ethanol on LNPs and gain a dynamic understanding of its impact on the overall structure and stability of LNPs. Our results demonstrate that ethanol destabilizes LNP structure over time, indicated by increased root mean square deviation (RMSD) values. Changes in the solvent-accessible surface area (SASA), electron density, and radial distribution function (RDF) also suggest that ethanol affects LNP stability. Furthermore, our H-bond profile analysis shows that ethanol penetrates the LNP earlier than water. These findings emphasize the importance of immediate ethanol removal in lipid-based systems during LNP production to ensure stability. Full article
(This article belongs to the Special Issue Recent Advances in Molecular Computational Chemistry)
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17 pages, 6671 KiB  
Article
Computational Insights into the Dynamic Structural Features and Binding Characteristics of Recombinase UvsX Compared with RecA
by Yue Pan, Ningkang Xie, Xin Zhang, Shuo Yang and Shaowu Lv
Molecules 2023, 28(8), 3363; https://doi.org/10.3390/molecules28083363 - 11 Apr 2023
Cited by 1 | Viewed by 1866
Abstract
RecA family recombinases are the core enzymes in the process of homologous recombination, and their normal operation ensures the stability of the genome and the healthy development of organisms. The UvsX protein from bacteriophage T4 is a member of the RecA family recombinases [...] Read more.
RecA family recombinases are the core enzymes in the process of homologous recombination, and their normal operation ensures the stability of the genome and the healthy development of organisms. The UvsX protein from bacteriophage T4 is a member of the RecA family recombinases and plays a central role in T4 phage DNA repair and replication, which provides an important model for the biochemistry and genetics of DNA metabolism. UvsX shares a high degree of structural similarity and function with RecA, which is the most deeply studied member of the RecA family. However, the detailed molecular mechanism of UvsX has not been resolved. In this study, a comprehensive all-atom molecular dynamics simulation of the UvsX protein dimer complex was carried out in order to investigate the conformational and binding properties of UvsX in combination with ATP and DNA, and the simulation of RecA was synchronized with the property comparison learning for UvsX. This study confirmed the highly conserved molecular structure characteristics and catalytic centers of RecA and UvsX, and also discovered differences in regional conformation, volatility and the ability to bind DNA between the two proteins at different temperatures, which would be helpful for the subsequent understanding and application of related recombinases. Full article
(This article belongs to the Special Issue Recent Advances in Molecular Computational Chemistry)
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16 pages, 8576 KiB  
Article
Probing the Mechanisms of Inhibitors Binding to Presenilin Homologue Using Molecular Dynamics Simulations
by Min Wang, Kaifeng Liu, Yingying Ma and Weiwei Han
Molecules 2023, 28(5), 2076; https://doi.org/10.3390/molecules28052076 - 22 Feb 2023
Cited by 5 | Viewed by 1749
Abstract
γ-secretase is an intramembrane proteolytic enzyme that is mainly involved in the cleavage and hydrolysis of the amyloid precursor (APP). The catalytic subunit presenilin 1 (PS1) is the catalytic subunit of γ-secretase. Since it was found that PS1 is responsible for Aβ-producing proteolytic [...] Read more.
γ-secretase is an intramembrane proteolytic enzyme that is mainly involved in the cleavage and hydrolysis of the amyloid precursor (APP). The catalytic subunit presenilin 1 (PS1) is the catalytic subunit of γ-secretase. Since it was found that PS1 is responsible for Aβ-producing proteolytic activity, which is involved in Alzheimer’s disease, it is believed that reducing the activity of PS1 and preventing or delaying the production of Aβ could help treat Alzheimer’s disease. Consequently, in recent years, researchers have begun investigating the potential clinical efficacy of PS1 inhibitors. Currently, most PS1 inhibitors are only used as a tool to study the structure and function of PS1, and a few inhibitors with a high selectivity have been tested in clinics. Less-selective PS1 inhibitors were found to not only inhibit Aβ production but also inhibit Notch cleavage, which led to serious adverse events. The archaeal presenilin homologue (PSH) is a surrogate protease of presenilin that is useful for agent screening. In this study, we performed 200 ns molecular dynamics simulations (MD) of four systems to explore the conformational changes of different ligands binding to PSH. Our results indicated that the PSH-L679 system formed 3–10 helices in TM4, loosening up TM4 and allowing substrates to enter the catalytic pocket, thereby making it less inhibitory. Additionally, we found that III-31-C can bring TM4 and TM6 closer, resulting in the contraction of the PSH active pocket. Altogether, these results provide the basis for the potential design of newer PS1 inhibitors. Full article
(This article belongs to the Special Issue Recent Advances in Molecular Computational Chemistry)
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14 pages, 1187 KiB  
Article
Experimental FTIR-MI and Theoretical Studies of Isocyanic Acid Aggregates
by Justyna Krupa, Maria Wierzejewska and Jan Lundell
Molecules 2023, 28(3), 1430; https://doi.org/10.3390/molecules28031430 - 2 Feb 2023
Cited by 1 | Viewed by 2144
Abstract
Homoaggregates of isocyanic acid (HNCO) were studied using FTIR spectroscopy combined with a low-temperature matrix isolation technique and quantum chemical calculations. Computationally, the structures of the HNCO dimers and trimers were optimized at the MP2, B3LYPD3 and B2PLYPD3 levels of theory employing the [...] Read more.
Homoaggregates of isocyanic acid (HNCO) were studied using FTIR spectroscopy combined with a low-temperature matrix isolation technique and quantum chemical calculations. Computationally, the structures of the HNCO dimers and trimers were optimized at the MP2, B3LYPD3 and B2PLYPD3 levels of theory employing the 6-311++G(3df,3pd) basis set. Topological analysis of the electron density (AIM) was used to identify the type of non-covalent interactions in the studied aggregates. Five stable minima were located on the potential energy surface for (HNCO)2, and nine were located on the potential energy surface for (HNCO)3. The most stable dimer (D1) involves a weak, almost linear N-H⋯N hydrogen bond. Other structures are bound by a N-H⋯O hydrogen bond or by O⋯C or N⋯N van der Waals interactions. Similar types of interactions as in (HNCO)2 were found in the case of HNCO trimers. Among nine stable (HNCO)3 structures, five represent cyclic forms. The most stable T1 trimer structure is characterized by a six-membered ring formed by three N-H⋯N hydrogen bonds and representing high symmetry (C3h). The analysis of the HNCO/Ar spectra after deposition indicates that the N-H⋯O hydrogen-bonded dimers are especially prevalent. Upon annealing, HNCO trimers were observed as well. Identification of the experimentally observed species relied on previous experimental data on HNCO complexes as well as computed data on HNCO homoaggregates’ vibrational spectra. Full article
(This article belongs to the Special Issue Recent Advances in Molecular Computational Chemistry)
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12 pages, 4647 KiB  
Article
Exploration of the Product Specificity of chitosanase CsnMY002 and Mutants Using Molecular Dynamics Simulations
by Jianzhang Lu, Chu Wang, Yingying Ma, Kaifeng Liu, Xueqi Fu and Shu Xing
Molecules 2023, 28(3), 1048; https://doi.org/10.3390/molecules28031048 - 20 Jan 2023
Cited by 2 | Viewed by 1771
Abstract
Chitosanase CsnMY002 is a new type of enzyme isolated from Bacillus subtilis that is used to prepare chitosan oligosaccharide. Although mutants G21R and G21K could increase Chitosan yield and thus increase the commercial value of the final product, the mechanism by which this [...] Read more.
Chitosanase CsnMY002 is a new type of enzyme isolated from Bacillus subtilis that is used to prepare chitosan oligosaccharide. Although mutants G21R and G21K could increase Chitosan yield and thus increase the commercial value of the final product, the mechanism by which this happens is not known. Herein, we used molecular dynamics simulations to explore the conformational changes in CsnMY002 wild type and mutants when they bind substrates. The binding of substrate changed the conformation of protein, stretching and deforming the active and catalytic region. Additionally, the mutants caused different binding modes and catalysis, resulting in different degrees of polymerization of the final Chitooligosaccharide degradation product. Finally, Arg37, Ile145 ~ Gly148 and Trp204 are important catalytic residues of CsnMY002. Our study provides a basis for the engineering of chitosanases. Full article
(This article belongs to the Special Issue Recent Advances in Molecular Computational Chemistry)
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18 pages, 6450 KiB  
Article
The Inhibitory Mechanism of 7H-Pyrrolo[2,3-d]pyrimidine Derivatives as Inhibitors of P21-Activated Kinase 4 through Molecular Dynamics Simulation
by Juan Du, Song Wang, Xinyue Zhang, Chang Liu, Yurou Zhang and Hao Zhang
Molecules 2023, 28(1), 413; https://doi.org/10.3390/molecules28010413 - 3 Jan 2023
Cited by 2 | Viewed by 2017
Abstract
The overexpression of p21-activated kinase 4 (PAK4) is associated with a variety of cancers. In this paper, the binding modes and inhibitory mechanisms of four 7H-pyrrolo[2,3-d]pyrimidine competitive inhibitors of PAK4 were investigated at the molecular level, mainly using molecular dynamics simulations [...] Read more.
The overexpression of p21-activated kinase 4 (PAK4) is associated with a variety of cancers. In this paper, the binding modes and inhibitory mechanisms of four 7H-pyrrolo[2,3-d]pyrimidine competitive inhibitors of PAK4 were investigated at the molecular level, mainly using molecular dynamics simulations and binding free energy calculations. The results show that the inhibitors had strong interactions with the hinge region, the β-sheets, and the residues with charged side chains around the 4-substituent. The terminal amino group of the inhibitor 5n was different from the other three, which could cause the enhancement of hydrogen bonds or electrostatic interactions formed with the surrounding residues. Thus, inhibitor 5n had the strongest inhibition capacity. The different halogen atoms on the 2-substituents of the inhibitors 5h, 5g, and 5e caused differences in the positions of the 2-benzene rings and affected the interactions of the hinge region. It also affected to some extent the orientations of the 4-imino groups and consequently their affinities for the surrounding charged residues. The combined results lead to the weakest inhibitory capacity of inhibitor 5e. Full article
(This article belongs to the Special Issue Recent Advances in Molecular Computational Chemistry)
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